Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
VDR

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCaP
tissue
LNCaP
cell line
LNCaP
cell type
WT
genotype
European American prostate cancer
chip antibody
VDR
treatment
Vehicle

Sequenced DNA Library

library_name
GSM6900288
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, approximately 20x106 cells were crosslinked with 1% formaldehyde solution, quenched with glycine (0.125 M) and harvested in cold PBS. Sonication of crosslinked chromatin was performed using a Bioruptor® UCD-200TM Sonicator (Diagenode) with optimized cycles for each cell type. Immunoprecipitation of sonicated material was performed with antibodies against VDR (D2K6W) – Cell Signaling) or IgG (Rabbit IgG sc2729 – Santa Cruz) for 16 hours, and antibody/bead complexes isolated with Magna ChIPTM Protein A+G magnetic beads (Millipore). Complexes were washed, reverse crosslinked, and treated sequentially with RNase and proteinase K prior to DNA isolation. Sequencing libraries prepared from immunopreciptiated DNA

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
1283610
Reads aligned (%)
0.0
Duplicates removed (%)
4.2
Number of peaks
20 (qval < 1E-05)

hg19

Number of total reads
1283610
Reads aligned (%)
0.0
Duplicates removed (%)
4.3
Number of peaks
22 (qval < 1E-05)

Base call quality data from DBCLS SRA